The present world scenario faces a serious threat from increasing dependence on fossil fuels. This has triggered the awareness to find alternative energy as their sustainable energy sources. Biodiesel as a cleaner renewable fuel may be considered as a good substitution for diesel fuel due to it being used in any compression ignition engine without any modification. The main advantages of using biodiesel are its renewability and better quality of exhaust gas emissions. In terms of emissions from biodiesel, the cause of concern continues to be the NOx emissions. Therefore, to compliment the functioning of biodiesels, Urea-SCR over Cu-ZSM5 catalyst is an effective option due to its ability to convert NOx into nitrogen and water. There has been increasing concerns that biodiesel feedstock may compete with food supply in the long term. The recent paper focuses on use of two non-edible oils mahua oil and fish oil (processed from waste produced by fish). The acid number of fish oil was found to be lower than mahua oil. Hence, the base catalyzed transesterification process was employed for production of fish oil methyl ester. On the other hand, mahua oil due to its higher free fatty acid content was esterified first and then, transesterified. B20 blend of biodiesels were used since it balances the property differences with conventional diesel e.g. performance, emission benefits and cost. Further, B20 blend can be used in automotive engines with no major modification. The present study focuses on the comparison of performance and emission characteristics of mahua oil biodiesel blends and fish oil biodiesel blends with diesel along with the employment of Urea-SCR as an exhaust treatment technology. The urea injection points have been varied along the exhaust pipe to study the dependence of distance between the engine exhaust and the SCR catalyst on the NOx emissions. The result shows the greater reduction of NOx for fish oil biodiesel and the brake thermal efficiency of fish oil biodiesel was found to be higher.